Among the churches he pastored was the Sixth Avenue Bible Baptist Church in Brooklyn, New York with Fanny J. Crosby as a member and they wrote many hymns together. Also,New Jersey was the Park Avenue Baptist Church. When the Park Avenue Church agreed to merge with the First Baptist church, Pastor Lowry agreed to resign in order to ensure the success of the merger. The merged church still exists as the First-Park Baptist Church in Plainfield, New Jersey.

In 1869 he returned to Lewisburg, Pennsylvania as a faculty member (having previously served as a professor of literature) and later went on to become its chancellor.

From 1880 until 1886 he was president of the New Jersey Baptist Sunday School Union.

Despite his success as a hymn writer, it was as a preacher that Lowry would have preferred to be recognised. He once stated: "Music, with me has been a side issue... I would rather preach a gospel sermon to an appreciative audience than write a hymn. I have always looked upon myself as a preacher and felt a sort of depreciation when I began to be known more as a composer."[2] However, it is as a hymn writer that he remains renowned.

A bronze plaque in the Plainfield, New Jersey was installed in 1911 to commemorate his dedication and service.[4] Original papers and hymns can be found at the church and also at the Plainfield Public Library.